bootstrap_simulated_plot: Bootstrap and plot simulated epidemic

In OJWatson/paper: Demonstration of analysis associated to "paper outbreak" teaching practical

Description

bootstrap_simulated_plot takes output of first_infection_list and outbreak_dataset_read and uses discrete_SIR_simulator to simulate a number of SIR epidemics, which are then summarised and plotted. Returns ggplot object for plotting.

Usage

bootstrap_simulated_plot(R0 = 1.8, I = 3, first_infection_list,
  outbreak.dataset, replicates = 2000, sampling = FALSE,
  lower.quantile = 0.25, upper.quantile = 0.75, title = NULL,
  alpha = 0.2, size = 1, include.line = TRUE, include.observed = FALSE,
  exponential = FALSE)

Arguments

R0	Reproductive number. Default = 1.8
I	Number of initial seed infections. Default = 3
first_infection_list	Infection list outputted by first_infection_list
outbreak.dataset	Outbreak dataset outputted by outbreak_dataset_read
replicates	Numerical describing number of bootstrap replicates. Default = 2000
sampling	Boolean determining if recovery and generation times should be sampled from the observed or drawn fro a poisson with mean equal to mean of the observed. Default = FALSE (poisson draws used)
lower.quantile	Numeric between 0 and 0.5 describing the lower quantile for each trace. Default = 0.25
upper.quantile	Numeric between 0.5 and 1 describing the lower quantile for each trace. Default = 0.75
title	Plot title. If NULL then no title will be added. Defult = NULL
alpha	Translucency of quantiles. Default = 0.2
size	Line width. Default = 1
include.line	Boolean describing whether to plot with the line or just the quantiles. Default = TRUE
include.observed	Boolean describing whether to include the observed epidemic alongisde the simulated epidemic. If this is true, N will be calculated from outbreak.dataset
exponential	Boolean determining if infection is exponential or not within the simulation. If FALSE (Default) then the number of secondary infections from an individual is takes into account S/N

OJWatson/paper documentation built on May 7, 2019, 8:33 p.m.